Clear "glass" bottle loses clearness in front of colored background
I have had this issue before. I am guessing the problem is with light paths in render settings.  If you don't have enough bounces, then having multiple transparent materials stacked behind one another will cause the darkening.

I'm pretty sure all I had to do was increase my minimum light bounces and it was fixed.  Good luck!

Edit: Minimum light bounces for transparency is the one you want to increase